Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:29 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 106/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ATACseqQC 1.28.0 (landing page) Jianhong Ou
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the ATACseqQC package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: ATACseqQC |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ATACseqQC_1.28.0.tar.gz |
StartedAt: 2024-05-06 19:41:20 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 19:45:20 -0400 (Mon, 06 May 2024) |
EllapsedTime: 240.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ATACseqQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ATACseqQC_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/ATACseqQC.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ATACseqQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ATACseqQC’ version ‘1.28.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ATACseqQC’ can be installed ... OK * checking installed package size ... NOTE installed size is 12.4Mb sub-directories of 1Mb or more: extdata 12.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed enrichedFragments 21.070 2.222 23.328 splitGAlignmentsByCut 8.269 0.289 8.563 distanceDyad 8.283 0.129 8.417 factorFootprints 8.109 0.181 8.293 vPlot 6.463 0.095 6.556 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/ATACseqQC.Rcheck/00check.log’ for details.
ATACseqQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ATACseqQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘ATACseqQC’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ATACseqQC)
ATACseqQC.Rcheck/tests/runTests.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("ATACseqQC") || stop("unable to load Package:ATACseqQC") Loading required package: ATACseqQC Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': expand.grid, I, unname [1] TRUE > require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments") Loading required package: GenomicAlignments Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools [1] TRUE > require("BSgenome") || stop("unable to load Package:BSgenome") Loading required package: BSgenome Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat [1] TRUE > require("rtracklayer") || stop("unable to load Package:rtracklayer") [1] TRUE > require("utils") || stop("unable to load Package:utils") [1] TRUE > require("testthat") || stop("unable to load testthat") Loading required package: testthat [1] TRUE > test_check("ATACseqQC") | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_factorFootprints.R:1:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ] > > proc.time() user system elapsed 28.282 0.712 28.988
ATACseqQC.Rcheck/ATACseqQC-Ex.timings
name | user | system | elapsed | |
NFRscore | 0.490 | 0.020 | 0.512 | |
PTscore | 0.805 | 0.009 | 0.813 | |
TSSEscore | 0.292 | 0.010 | 0.303 | |
bamQC | 0.983 | 0.024 | 1.007 | |
distanceDyad | 8.283 | 0.129 | 8.417 | |
enrichedFragments | 21.070 | 2.222 | 23.328 | |
estimateLibComplexity | 1.043 | 0.008 | 1.051 | |
factorFootprints | 8.109 | 0.181 | 8.293 | |
footprintsScanner | 3.322 | 0.288 | 3.620 | |
fragSizeDist | 0.206 | 0.009 | 0.217 | |
plotCorrelation | 0.447 | 0.016 | 0.463 | |
plotFootprints | 0.171 | 0.004 | 0.176 | |
pseudoPausingIndex | 0.395 | 0.006 | 0.401 | |
readBamFile | 0.287 | 0.022 | 0.308 | |
readsDupFreq | 0.281 | 0.005 | 0.286 | |
saturationPlot | 0 | 0 | 0 | |
shiftGAlignments | 3.820 | 0.231 | 4.053 | |
shiftGAlignmentsList | 2.009 | 0.092 | 2.101 | |
splitBam | 0 | 0 | 0 | |
splitGAlignmentsByCut | 8.269 | 0.289 | 8.563 | |
vPlot | 6.463 | 0.095 | 6.556 | |
writeListOfGAlignments | 0.069 | 0.005 | 0.074 | |